Associate Professor at the Biochemistry and Biotechnology Department, URV

1996-1999:

PhD degree in Biochemistry (URV). PhD Fellow from the Generalitat de Catalunta (FIAP/96-7.030)

1990-1995:

B.Sc degree in Chemistry (URV). Fellowship from the Ministerio de Educación y Ciencia to collaborate with the Biochemistry and Biotechnology Department (URV) (B.O.E. no 108, 6 de mayo de 1995, pág. 13219).

MERITS RELATED TO RESEARCH/ACADEMIC ACTIVITY

SER-LAB prize at 1995 to the student with the best academic expedient integrated in a research group of the Faculty of Chemistry of the URV

Participant of the BioROM (learning material to biochemistry, biotechnology and molecular biology)

Member of the Scientific Committee of the organization of the congress of the Spanish Society of Evolutionary Biology. Tarragona, 27-29th September 2007

Evaluation favorable at the Recognition Program Quality Research (RQR) of the Rovira i Virgili University that identifies the scientist with a research activity that has an impact on quality significantly higher than the world average in his/her research field. Since 2011-12 to 2014-15

In my beginning as a researcher, I was introduced to the fields of Bioinformatics and sequence analysis. My PhD thesis was centered in the analysis of bacterial complete genomes and in the detection, using computational tools, of horizontally transferred genes. My post-doctoral stay for 5 months in the European Bioinformatics Institute (EBI) in Cambridge, UK, helped me to acquire a solid formation in programming and bioinformatics. With my research team, we published several articles in prestigious international journals, such as Nucleic Acids Research, Trends in Genetics, Trends in Microbiology, Genome Research, Bioinformatics and Molecular Biology and Evolution. I also developed several databases, web-servers and tools for the prediction of horizontally transferred genes and highly expressed genes, the analysis of codon usage bias, codon adaptation and codon usage optimization in bacterial genes and genomes. With my integration, in 2009, to the Nutrigenomics group at the Biochemistry and Biotechnology Department of the Rovira i Virgili University, I changed my research focus to Cheminformatics and the search and characterization of new ingredients for functional foods. Now, I belong to the Cheminformatics and Nutrition Group at the Biochemistry and Biotechnology Department of the Rovira i Virgili University. Our aim is, using a similar methodology used in the field of computational drug design, to search for natural compounds that can activate or inhibit certain molecular targets, such enzymes and transcription factors, and be potential new ingredients in the food industry to develop new functional foods (a food given an additional function, often one related to health-promotion or disease prevention).

In the field of developing new antidiabetics, we have contributed to the analysis of the differences between full and partial agonists of PPARgamma and we have developed a virtual screening procedure to search for new partial agonists of PPARgamma. Using this procedure we have demonstrated that several natural compounds act as antidiabetic compounds, reducing the insulin resistance associated with the diabetes type II, because they bind and activate the nuclear receptor PPARgamma. In addition, our research group have found new antidiabetic compounds that inhibit the dipeptidyl peptidase-4 (DPP4) and new anti-inflammatory compounds that inhibit the inhibitor of nuclear factor kappa-B kinase subunit beta (IKK2). We have also developed several new cheminformatic tools for helping the virtual screening process, for example for finding decoys and validate the models of crystallized protein structures. Our results have been published in prestigious international journals, such as Journal of Medicinal Chemistry, Methods, Journal of Cheminformatics, Plos One, Journal of Computer-Aided Molecular Design, and European Journal of Medicinal Chemistry. We have been funded by the Spanish Government with the project AGL2011-25831 and by some enterprise projects.

The Validation HElper for LIgands and Binding Sites (VHELIBS) aims to ease the validation of binding site and ligand coordinates for non-crystallographers (i.e. users with little or no crystallography knowledge) by checking how their coordinates fit to their corresponding electron density map and letting the user to use models from either the PDB or PDB_REDO. The user can specify threshold values for a series of properties related with coordinates to electron density fitting (where Real Space R, Real Space Correlation Coefficient and average occupancy are the ones used by default) and, VHELIBS will automatically label residues and ligands with values within the specified limits, and the rest as either dubious or bad based on an user-configurable tolerance value. The user then is able to visually check the fitness quality of the residues/ligands to their corresponding electron density map, and reclassify them if needed.

DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set.

The RCDI server is a web-application that calculates the Relative Codon Deoptimization Index (RCDI) and an expected value of the RCDI for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected RCDI therefore provides a direct threshold value for discerning whether the differences in the RCDI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences. Please, click here to get a quick tutorial.

This server performs several computations in relation to codon usage and the codon adaptation of DNA or RNA sequences to host organisms. The E-CAI server is a web-application and an executable program that calculates the expected value of the Codon Adaptation Index (CAI) for a set of query sequences by generating random sequences with similar G+C content and amino acid composition to the input. This expected CAI therefore provides a direct threshold value for discerning whether the differences in the CAI value are statistically significant and arise from the codon preferences or whether they are merely artifacts that arise from internal biases in the G+C composition and/or amino acid composition of the query sequences.

The HEG-DB is a genomic database that includes the prediction of which genes are highly expressed in prokaryotic complete genomes under strong translational selection. The current version of the database contains general features for almost 200 genomes under translational selection, including the correspondence analysis of the relative synonymous codon usage for all genes, and the analysis of their highly expressed genes. For each genome, the database contains functional and positional information about the predicted group of highly expressed genes. This information can also be accessed using a search engine. Among other statistical parameters, the database also provides the Codon Adaptation Index for all of the genes using the codon usage of the highly expressed genes as a reference set. The "Pathway Tools Omics Viewer" from the BioCyc database enables the metabolic capabilities of each genome to be explored, particularly those related to the group of highly expressed genes.

OPTIMIZER is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level. Users can introduce their own preference tables to be used in the optimization process or use pre-computed tables from several prokaryotic species under a strong translational selection. Three methods of optimization are available: the 'one amino acid - one codon' approach, a random approach or an intermediate one. Several options, such as avoiding specific restriction sites and several outputs, are also available. This server can be useful for predicting and optimizing the level expression of a gene in heterologous gene expression.

TOPD/FMTS is a new software for comparing phylogenetic trees. It has been developed to calculate the differences between trees. The software implements several previously described methods and new algorithms for comparing phylogenetic trees. It combines the TOPD program (TOPological Distance), which compares two trees with the same taxa or two pruned trees, and the FMTS program (From Multiple To Single), which converts multi-gene family trees to single-gene trees.

The HGT-DB is a genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer. The current version of the database includes the analysis of 94 bacterial and archaeal complete genomes, including multiple chromosomes and strains, when available. Other complete genomes will be added progressively.

Use this program to create a dendrogram from a set of variables. The program calculates a similarity coefficient between pairs of sets of variables, transforms these coefficients into distances and makes a clustering using the Unweighted Pair Group Method with Arithmetic mean (UPGMA) algorithm.

"A general view of computational methods for target fishing and focus on the use of fingerprints for chemical similarity searching". International Work-Conference on Bioinformatics and Biomedical Engineering. Granada, 20-22th April 2016